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- PDB-2n2q: NMR solution structure of HsAFP1 -

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Basic information

Entry
Database: PDB / ID: 2n2q
TitleNMR solution structure of HsAFP1
ComponentsDefensin-like protein 1
KeywordsANTIFUNGAL PROTEIN
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism / extracellular region
Similarity search - Function
Defensin, plant / Gamma-thionins family signature. / Gamma-thionin family / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Defensin-like protein 1
Similarity search - Component
Biological speciesHeuchera sanguinea (coralbells)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHarvey, P.J. / Craik, D.J. / Vriens, K.
CitationJournal: Plos One / Year: 2015
Title: Synergistic Activity of the Plant Defensin HsAFP1 and Caspofungin against Candida albicans Biofilms and Planktonic Cultures.
Authors: Vriens, K. / Cools, T.L. / Harvey, P.J. / Craik, D.J. / Spincemaille, P. / Cassiman, D. / Braem, A. / Vleugels, J. / Nibbering, P.H. / Drijfhout, J.W. / De Coninck, B. / Cammue, B.P. / Thevissen, K.
History
DepositionMay 11, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defensin-like protein 1


Theoretical massNumber of molelcules
Total (without water)5,9591
Polymers5,9591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Defensin-like protein 1 / Cysteine-rich antifungal protein 1 / Defensin AFP1 / HsAFP1


Mass: 5958.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heuchera sanguinea (coralbells) / Production host: Pichia pastoris (fungus) / References: UniProt: P0C8Y5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-15N HSQC
1422D 1H-13C HSQC
1522D E-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM protein, 90% H2O/10% D2O90% H2O/10% D2O
21 mM protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMentity-11
1 mMentity-22
Sample conditionspH: 4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CCPNmrCCPNchemical shift assignment
CCPNmrCCPNpeak picking
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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